[English] 日本語
Yorodumi
- PDB-2obh: Centrin-XPC peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2obh
TitleCentrin-XPC peptide
Components
  • Centrin-2
  • DNA-repair protein complementing XP-C cells
KeywordsCELL CYCLE / DNA REPAIR COMPLEX EF HAND SUPERFAMILY PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / 9+2 motile cilium / nucleotide-excision repair complex / photoreceptor connecting cilium / DNA damage sensor activity / heterotrimeric G-protein binding / transcription export complex 2 ...heteroduplex DNA loop binding / pyrimidine dimer repair by nucleotide-excision repair / nucleotide-excision repair factor 2 complex / XPC complex / 9+2 motile cilium / nucleotide-excision repair complex / photoreceptor connecting cilium / DNA damage sensor activity / heterotrimeric G-protein binding / transcription export complex 2 / response to auditory stimulus / nuclear pore nuclear basket / bubble DNA binding / UV-damage excision repair / response to UV-B / mitotic intra-S DNA damage checkpoint signaling / regulation of mitotic cell cycle phase transition / centriole replication / site of DNA damage / glial cell projection / mRNA transport / mismatch repair / SUMOylation of DNA damage response and repair proteins / centriole / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / regulation of cytokinesis / nucleotide-excision repair / DNA Damage Recognition in GG-NER / G-protein beta/gamma-subunit complex binding / microtubule cytoskeleton organization / Formation of Incision Complex in GG-NER / apical part of cell / Regulation of PLK1 Activity at G2/M Transition / protein transport / mitotic cell cycle / single-stranded DNA binding / microtubule binding / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / transcription coactivator activity / ciliary basal body / response to xenobiotic stimulus / cell division / DNA repair / intracellular membrane-bounded organelle / centrosome / calcium ion binding / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / nucleolus / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rad4 beta-hairpin domain 2 / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 ...Rad4 beta-hairpin domain 2 / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / : / Transglutaminase-like superfamily / ATP-dependent RNA helicase DEAD-box, conserved site / EF-hand / Recoverin; domain 1 / Papain-like cysteine peptidase superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Centrin-2 / DNA repair protein complementing XP-C cells
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCharbonnier, J.B.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structural, thermodynamic, and cellular characterization of human centrin 2 interaction with xeroderma pigmentosum group C protein.
Authors: Charbonnier, J.B. / Renaud, E. / Miron, S. / Le Du, M.H. / Blouquit, Y. / Duchambon, P. / Christova, P. / Shosheva, A. / Rose, T. / Angulo, J.F. / Craescu, C.T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray diffraction data of the complex between human centrin 2 and a peptide from the protein XPC
Authors: Charbonnier, J.B. / Christova, P. / Shosheva, A. / Le Du, E. / Stura, M.H. / Blouquit, Y. / Duchambon, P. / Miron, S. / Craescu, C.T.
#2: Journal: Biochemistry / Year: 2006
Title: Flexibility and plasticity of human centrin 2 binding to the xeroderma pigmentosum group C protein (XPC) from nuclear excision repair
Authors: Yang, A. / Miron, S. / Mouawad, L. / Duchambon, P. / Blouquit, Y. / Craescu, C.T.
#3: Journal: J.Biol.Chem. / Year: 2006
Title: The structure of the human centrin 2-xeroderma pigmentosum group C protein complex
Authors: Thompson, J.R. / Ryan, Z.C. / Salisbury, J.L. / Kumar, R.
History
DepositionDec 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Centrin-2
B: Centrin-2
C: DNA-repair protein complementing XP-C cells
D: DNA-repair protein complementing XP-C cells
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4238
Polymers37,2634
Non-polymers1604
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.278, 59.419, 105.137
Angle α, β, γ (deg.)90.00, 94.67, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14C
24D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUASNASNAA27 - 852 - 60
21GLUGLUASNASNBB27 - 852 - 60
12PHEPHEPHEPHEAA86 - 11361 - 88
22PHEPHEPHEPHEBB86 - 11361 - 88
13ASPASPILEILEAA114 - 16589 - 140
23ASPASPILEILEBB114 - 16589 - 140
14ASNASNLYSLYSCC847 - 8622 - 17
24ASNASNLYSLYSDD847 - 8622 - 17

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein Centrin-2 / Caltractin isoform 1


Mass: 16491.637 Da / Num. of mol.: 2 / Fragment: HsCen2 ( Residues: 26-168)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CETN2, CALT, CEN2 / Plasmid: PET24A(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41208
#2: Protein/peptide DNA-repair protein complementing XP-C cells / Xeroderma pigmentosum group C-complementing protein / p125


Mass: 2139.677 Da / Num. of mol.: 2 / Fragment: XPC fragment (Residues: 847-863) / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS IN HOMO SAPIENS / References: UniProt: Q01831
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 30% MPEG 550, 0.1M NaCl, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.8→52.4 Å / Num. obs: 34221 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 20.95 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 17.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4768 / Rsym value: 0.395 / % possible all: 95.5

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TOP

1top


Resolution: 1.8→52.4 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.353 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1722 5 %RANDOM
Rwork0.201 ---
all0.231 32734 --
obs0.205 32499 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.348 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.37 Å2
2---0.74 Å20 Å2
3---0.55 Å2
Refine analyzeLuzzati coordinate error obs: 0.237 Å
Refinement stepCycle: LAST / Resolution: 1.8→52.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 4 384 2979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222615
X-RAY DIFFRACTIONr_angle_refined_deg1.4052.0023470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4665315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76626.183131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51315585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.221515
X-RAY DIFFRACTIONr_chiral_restr0.1050.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021889
X-RAY DIFFRACTIONr_nbd_refined0.2190.21381
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21810
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2308
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.256
X-RAY DIFFRACTIONr_mcbond_it1.1181.51651
X-RAY DIFFRACTIONr_mcangle_it1.69622528
X-RAY DIFFRACTIONr_scbond_it2.64331071
X-RAY DIFFRACTIONr_scangle_it4.0924.5942
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A468MEDIUM POSITIONAL0.330.5
1A468MEDIUM THERMAL0.662
2A232MEDIUM POSITIONAL0.440.5
2A232MEDIUM THERMAL1.222
3A417MEDIUM POSITIONAL0.430.5
3A417MEDIUM THERMAL0.692
4C137MEDIUM POSITIONAL0.550.5
4C137MEDIUM THERMAL1.132
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 111 -
Rwork0.253 2243 -
obs-2354 92.17 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1009-0.1116-0.0731.44291.01530.7322-0.0194-0.00530.00220.03470.051-0.01660.0280.0285-0.0316-0.00160.008-0.0002-0.02770.03860.03366.0115.66225.919
20.1135-0.0448-0.09411.65470.85590.87820.0085-0.00240.02870.07690.08-0.2739-0.0069-0.0314-0.0885-0.00040.0151-0.0319-0.04080.0054-0.0042.07115.93726.174
30.06770.175-0.61380.529-1.50855.6496-0.0589-0.0422-0.02180.0915-0.1371-0.1267-0.33670.22810.19610.0223-0.0016-0.00720.0154-0.00220.01965.88715.88726.178
40.53510.215-2.5290.2552-0.713912.4933-0.05360.05580.0135-0.0069-0.26-0.1841-0.3117-0.250.31360.0005-0.0012-0.0054-0.00010.00090.0004-2.5715.83126.214
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA27 - 852 - 60
21BB27 - 852 - 60
32AA86 - 11361 - 88
42BB86 - 11361 - 88
53AA114 - 16589 - 140
63BB114 - 16589 - 140
74CC847 - 8622 - 17
84DD847 - 8622 - 17

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more